niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tto1_d.py

@@ -0,0 +1,246 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TTO1_D_METADATA = Metadata(
+    id="c4536089d729353b2214d75b62553c23db962d0e.boutiques",
+    name="3dTto1D",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTto1DParameters = typing.TypedDict('V3dTto1DParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTto1D"],
+    "input_dataset": InputPathType,
+    "method": str,
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbose": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTto1D": v_3d_tto1_d_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dTto1D": v_3d_tto1_d_outputs,
+    }.get(t)
+
+
+class V3dTto1DOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tto1_d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output 1D time series file"""
+
+
+def v_3d_tto1_d_params(
+    input_dataset: InputPathType,
+    method: str,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    verbose: float | None = None,
+) -> V3dTto1DParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Specify input dataset. This should be a set of 3D time\
+            series. If the input is in 1D format, a transpose operator will\
+            typically be required.
+        method: Specify 4D to 1D conversion method. Methods include: enorm,\
+            dvars, srms, shift_srms, mdiff, smdiff, 4095_count, 4095_frac,\
+            4095_warn.
+        automask: Restrict computation to automask.
+        mask: Restrict computation to given mask.
+        prefix: Specify output file. Default is stdout.
+        verbose: Specify verbose level. Default is 1.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTto1D",
+        "input_dataset": input_dataset,
+        "method": method,
+        "automask": automask,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def v_3d_tto1_d_cargs(
+    params: V3dTto1DParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dTto1D")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    cargs.extend([
+        "-method",
+        params.get("method")
+    ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    return cargs
+
+
+def v_3d_tto1_d_outputs(
+    params: V3dTto1DParameters,
+    execution: Execution,
+) -> V3dTto1DOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dTto1DOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tto1_d_execute(
+    params: V3dTto1DParameters,
+    execution: Execution,
+) -> V3dTto1DOutputs:
+    """
+    Collapse a 4D time series to a 1D time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTto1DOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tto1_d_cargs(params, execution)
+    ret = v_3d_tto1_d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tto1_d(
+    input_dataset: InputPathType,
+    method: str,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    verbose: float | None = None,
+    runner: Runner | None = None,
+) -> V3dTto1DOutputs:
+    """
+    Collapse a 4D time series to a 1D time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Specify input dataset. This should be a set of 3D time\
+            series. If the input is in 1D format, a transpose operator will\
+            typically be required.
+        method: Specify 4D to 1D conversion method. Methods include: enorm,\
+            dvars, srms, shift_srms, mdiff, smdiff, 4095_count, 4095_frac,\
+            4095_warn.
+        automask: Restrict computation to automask.
+        mask: Restrict computation to given mask.
+        prefix: Specify output file. Default is stdout.
+        verbose: Specify verbose level. Default is 1.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTto1DOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TTO1_D_METADATA)
+    params = v_3d_tto1_d_params(
+        input_dataset=input_dataset,
+        method=method,
+        automask=automask,
+        mask=mask,
+        prefix=prefix,
+        verbose=verbose,
+    )
+    return v_3d_tto1_d_execute(params, execution)
+
+
+__all__ = [
+    "V3dTto1DOutputs",
+    "V3dTto1DParameters",
+    "V_3D_TTO1_D_METADATA",
+    "v_3d_tto1_d",
+    "v_3d_tto1_d_params",
+]

niwrap_afni/afni/v_3d_twoto_complex.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TWOTO_COMPLEX_METADATA = Metadata(
+    id="bf9493b3c937b76d0584de14a9b270a71cce9ca0.boutiques",
+    name="3dTwotoComplex",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTwotoComplexParameters = typing.TypedDict('V3dTwotoComplexParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTwotoComplex"],
+    "dataset1": InputPathType,
+    "dataset2": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "ri": bool,
+    "mp": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTwotoComplex": v_3d_twoto_complex_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dTwotoComplex": v_3d_twoto_complex_outputs,
+    }.get(t)
+
+
+class V3dTwotoComplexOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_twoto_complex(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_brick: OutputPathType | None
+    """Output complex-valued dataset with prefix"""
+    out_head: OutputPathType | None
+    """Header for the complex-valued dataset"""
+
+
+def v_3d_twoto_complex_params(
+    dataset1: InputPathType,
+    dataset2: InputPathType | None = None,
+    prefix: str | None = None,
+    ri: bool = False,
+    mp: bool = False,
+    mask: InputPathType | None = None,
+) -> V3dTwotoComplexParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset1: Input dataset (either as 1 dataset with 2 sub-bricks or 2\
+            separate datasets).
+        dataset2: Second input dataset (optional if 2 sub-bricks in the first\
+            dataset).
+        prefix: Prefix for the output dataset [default='cmplx'].
+        ri: Specify that the 2 inputs are real and imaginary parts [this is the\
+            default].
+        mp: Specify that the 2 inputs are magnitude and phase [phase is in\
+            radians].
+        mask: Only output nonzero values where the mask dataset is nonzero.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTwotoComplex",
+        "dataset1": dataset1,
+        "ri": ri,
+        "mp": mp,
+    }
+    if dataset2 is not None:
+        params["dataset2"] = dataset2
+    if prefix is not None:
+        params["prefix"] = prefix
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_twoto_complex_cargs(
+    params: V3dTwotoComplexParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dTwotoComplex")
+    cargs.append(execution.input_file(params.get("dataset1")))
+    if params.get("dataset2") is not None:
+        cargs.append(execution.input_file(params.get("dataset2")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("ri"):
+        cargs.append("-RI")
+    if params.get("mp"):
+        cargs.append("-MP")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    return cargs
+
+
+def v_3d_twoto_complex_outputs(
+    params: V3dTwotoComplexParameters,
+    execution: Execution,
+) -> V3dTwotoComplexOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dTwotoComplexOutputs(
+        root=execution.output_file("."),
+        out_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_twoto_complex_execute(
+    params: V3dTwotoComplexParameters,
+    execution: Execution,
+) -> V3dTwotoComplexOutputs:
+    """
+    Converts 2 sub-bricks of input to a complex-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTwotoComplexOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_twoto_complex_cargs(params, execution)
+    ret = v_3d_twoto_complex_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_twoto_complex(
+    dataset1: InputPathType,
+    dataset2: InputPathType | None = None,
+    prefix: str | None = None,
+    ri: bool = False,
+    mp: bool = False,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dTwotoComplexOutputs:
+    """
+    Converts 2 sub-bricks of input to a complex-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset1: Input dataset (either as 1 dataset with 2 sub-bricks or 2\
+            separate datasets).
+        dataset2: Second input dataset (optional if 2 sub-bricks in the first\
+            dataset).
+        prefix: Prefix for the output dataset [default='cmplx'].
+        ri: Specify that the 2 inputs are real and imaginary parts [this is the\
+            default].
+        mp: Specify that the 2 inputs are magnitude and phase [phase is in\
+            radians].
+        mask: Only output nonzero values where the mask dataset is nonzero.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTwotoComplexOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TWOTO_COMPLEX_METADATA)
+    params = v_3d_twoto_complex_params(
+        dataset1=dataset1,
+        dataset2=dataset2,
+        prefix=prefix,
+        ri=ri,
+        mp=mp,
+        mask=mask,
+    )
+    return v_3d_twoto_complex_execute(params, execution)
+
+
+__all__ = [
+    "V3dTwotoComplexOutputs",
+    "V3dTwotoComplexParameters",
+    "V_3D_TWOTO_COMPLEX_METADATA",
+    "v_3d_twoto_complex",
+    "v_3d_twoto_complex_params",
+]